loop over files using extension, and have one argument be the file prefix (linux)

Question

I am trying to figure out a good way to make a for loop where I run a command over a set of files with the same extension, and use the file prefix of the same file as an argument. eg:

for i in *.vcf
do
   bionformatic_software -input $i -output_prefix $i without the .vcf extension 
done

Thanks in advance.